A New System for Comparative Functional Genomics of Saccharomyces Yeasts

Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var. uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae. We first created a suite of genetic tools to facilitate work in S. bayanus. Next, we measured the gene-expression response of S. bayanus to a diverse set of perturbations optimized using a computational approach to cover a diverse array of functionally relevant biological responses. The resulting data set reveals that gene-expression patterns are largely conserved, but significant changes may exist in regulatory networks such as carbohydrate utilization and meiosis. In addition to regulatory changes, our approach identified gene functions that have diverged. The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy. A surprising number of genes specific to S. bayanus respond to oxidative stress, suggesting the organism may have evolved under different selection pressures than S. cerevisiae. This work expands the scope of genome-scale evolutionary studies from sequence-based analysis to rapid experimental characterization and could be adopted for functional mapping in any lineage of interest. Furthermore, our detailed characterization of S. bayanus provides a valuable resource for comparative functional genomics studies in yeast.     

Molecular evolution of sex-biased genes in Drosophila

Studies of morphology, interspecific hybridization, protein/DNA sequences, and levels of gene expression have suggested that sex-related characters (particularly those involved in male reproduction) evolve rapidly relative to non-sex-related characters. Here we report a general comparison of evolutionary rates of sex-biased genes using data from cDNA microarray experiments and comparative genomic studies of Drosophila. Comparisons of nonsynonymous/synonymous substitution rates (d(N)/d(S)) between species of the D. melanogaster subgroup revealed that genes with male-biased expression had significantly faster rates of evolution than genes with female-biased or unbiased expression. The difference was caused primarily by a higher d(N) in the male-biased genes. The same pattern was observed for comparisons among more distantly related species. In comparisons between D. melanogaster and D. pseudoobscura, genes with highly biased male expression were significantly more divergent than genes with highly biased female expression. In many cases, orthologs of D. melanogaster male-biased genes could not be identified in D. pseudoobscura through a Blast search. In contrast to the male-biased genes, there was no clear evidence for accelerated rates of evolution in female-biased genes, and most comparisons indicated a reduced rate of evolution in female-biased genes relative to unbiased genes. Male-biased genes did not show an increased ratio of nonsynonymous/synonymous polymorphism within D. melanogaster, and comparisons of polymorphism/divergence ratios suggest that the rapid evolution of male-biased genes is caused by positive selection.     

被子植物小热激蛋白家族的比较基因组学分析

小热激蛋白(sHSP)是一类重要的响应外界环境变化以及调控植物生长发育的蛋白家族。基于在睡莲(Nymphaea colorata)、水稻(Oryza sativa)、拟南芥(Arabidopsis thaliana)和葡萄(Vitis vinifera)中分别鉴定到的33个NcsHSPs、24个OssHSPs、17个A...     

植物抗性基因研究新趋势

多种生物基因组的大规模测序结果表明,抗性基因在基因组上成簇存在,从结构基因组、比较基因组、功能基因组与生物信息学等方面论述了植物抗性基因研究的新趋势。     

启动以细胞为基本功能单元的系统人类基因转录组研究

基因组学、分子生物学和细胞生物学等基础生命科学领域前沿的概念和技术都在高速形成和发展,这些领域和新概念、新技术的不断融合推动生命科学研究从一个生长点到又一个新的生长点。人类基因组研究将在未来的五到十年里,从以一个基因组为对象的研究进入到以每个体基因组为对象的研究。基因功能和功能相关性的研究也将进入到以细胞为单元的研究,转录组研究必将成为这一研究的基础和出发点。转录组研究包括转录组的构成、调控和与蛋白质组的关联等基本部分,以及在临床诊断和药物研发中的应用。在生理状态下,每一种细胞中基因的共有和特异功能最终构成物种的生长、发育和演化。在病理状态下,每一种细胞中基因的变异和失控最终导致器官、组织、乃至个体的衰亡。人类转录组研究是基因功能研究的最基本层次之一,作为基因产物的RNA和蛋白质在这个层次上的存在、变化、关联和在细胞间的差异构成转录组研究的基本内容。     

Comparative genome assembly

One of the most complex and computationally intensive tasks of genome sequence analysis is genome assembly. Even today, few centres have the resources, in both software and hardware, to assemble a genome from the thousands or millions of individual sequences generated in a whole-genome shotgun sequencing project. With the rapid growth in the number of sequenced genomes has come an increase in the number of organisms for which two or more closely related species have been sequenced. This has created the possibility of building a comparative genome assembly algorithm, which can assemble a newly sequenced genome by mapping it onto a reference genome. We describe here a novel algorithm for comparative genome assembly that can accurately assemble a typical bacterial genome in less than four minutes on a standard desktop computer. The software is available as part of the open-source AMOS project.     

Validation of in silico-predicted genic SNPs in white clover (<Emphasis Type="Italic">Trifolium repens</Emphasis> L.), an outbreeding allopolyploid species

White clover (Trifolium repens L.) is an obligate outbreeding allotetraploid forage legume. Gene-associated SNPs provide the optimum genetic system for improvement of such crop species. An EST resource obtained from multiple cDNA libraries constructed from numerous genotypes of a single cultivar has been used for in silico SNP discovery and validation. A total of 58 from 236 selected sequence clusters (24.5%) were fully validated as containing polymorphic SNPs by genotypic analysis across the parents and progeny of several two-way pseudo-testcross mapping families. The clusters include genes belonging to a broad range of predicted functional categories. Polymorphic SNP-containing ESTs have also been used for comparative genomic analysis by comparison with whole genome data from model legume species, as well as Arabidopsis thaliana. A total of 29 (50%) of the 58 clusters detected putative ortholoci with known chromosomal locations in Medicago truncatula, which is closely related to white clover within the Trifolieae tribe of the Fabaceae. This analysis provides access to translational data from model species. The efficiency of in silico SNP discovery in white clover is limited by paralogous and homoeologous gene duplication effects, which are resolved unambiguously by the transmission test. This approach will also be applicable to other agronomically important cross-pollinating allopolyploid plant species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. N.O.I. Cogan and M.C. Drayton contributed equally to this work.